when you have a beacon effect on the player emits little swirly particles.if you stand next to water and look through a swirly particle into the water there will be no water inside the particle.
Tjhe same applies to lightning in front of ice or water
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Maybe it's a matter of mixing the alpha blending of the water/ice to the alpha blending of the particles. Snapshot 12w41a: Potion-like effects given by the Beacon now use semi-transparent particles, to be less intrusive.
Consolidiating all "transparent textures in front of another transparent texture" to MC-1379
Confirmed and also applies to ice and nether portals.